Package ubic.gemma.core.loader.expression.geo.model

Class GeoSeries

  • All Implemented Interfaces:
    Serializable
    public class GeoSeries
extends GeoData
    Represents a set of GEO samples that were submitted together. In many cases this corresponds to a full study, but for studies that used more than one type of microarray (e.g., A and B chips in Affy sets), there will be two series.
    Author:
    pavlidis
    See Also:
    Serialized Form

    • Constructor Detail

      • GeoSeries

        public GeoSeries()

    • Method Detail

      • convertStringToSeriesType

        public static GeoSeries.SeriesType convertStringToSeriesType​(String string)
        See also GeoDataset.convertStringToExperimentType
        Parameters:
        string - series type string
        Returns:
        series type object

      • addContributer

        public void addContributer​(GeoContact contributer)

      • addDataSet

        public void addDataSet​(GeoDataset dataset)

      • addSample

        public void addSample​(GeoSample sample)

      • addSamples

        public void addSamples​(Collection<GeoSample> s)
        Add a group of samples to this series.
        Parameters:
        s - samples

      • addSubSeries

        public void addSubSeries​(String value)

      • addToKeyWords

        public void addToKeyWords​(String keyword)

      • addToPubmedIds

        public void addToPubmedIds​(String id)
        Parameters:
        id - in format "1239954" or "1239954,2194919", etc. The latter will be split into two.

      • addToSummary

        public void addToSummary​(String text)
        Parameters:
        text - to add onto the summary. A space is added to the end of the previous summary first.

      • getSeriesId

        public String getSeriesId()

      • setSeriesId

        public void setSeriesId​(String seriesId)

      • getStatus

        public String getStatus()

      • setStatus

        public void setStatus​(String status)

      • getSubmissionDate

        public String getSubmissionDate()

      • setSubmissionDate

        public void setSubmissionDate​(String submissionDate)

      • getPlatformId

        public String getPlatformId()

      • setPlatformId

        public void setPlatformId​(String platformId)

      • setSubSeries

        public void setSubSeries​(boolean subSeries)

      • setSuperSeries

        public void setSuperSeries​(boolean superSeries)

      • getSummary

        public String getSummary()

      • setSummary

        public void setSummary​(String summary)

      • getContributers

        public Collection<GeoContact> getContributers()
        Returns:
        Returns the contributers.

      • setContributers

        public void setContributers​(Collection<GeoContact> contributers)
        Parameters:
        contributers - The contributers to set.

      • getKeyWords

        public Collection<String> getKeyWords()
        Returns:
        Returns the type.

      • setKeyWords

        public void setKeyWords​(Collection<String> type)
        Parameters:
        type - The type to set.

      • getLastUpdateDate

        public String getLastUpdateDate()
        Returns the date the series was last updated.
        Returns:
        String

      • setLastUpdateDate

        public void setLastUpdateDate​(String lastUpdateDate)
        Parameters:
        lastUpdateDate - the date the series was last updated.

      • getOverallDesign

        public String getOverallDesign()
        Returns:
        Returns the overallDesign.

      • setOverallDesign

        public void setOverallDesign​(String overallDesign)
        Parameters:
        overallDesign - The overallDesign to set.

      • getPubmedIds

        public Collection<String> getPubmedIds()
        Returns:
        Returns the pubmedIds.

      • setPubmedIds

        public void setPubmedIds​(Collection<String> pubmedIds)
        Parameters:
        pubmedIds - The pubmedIds to set.

      • setReplicates

        public void setReplicates​(Map<Integer,​GeoReplication> replicates)
        Parameters:
        replicates - The replicates to set.

      • getSampleCorrespondence

        public GeoSampleCorrespondence getSampleCorrespondence()
        Returns:
        Returns the sampleCorrespondence.

      • setSampleCorrespondence

        public void setSampleCorrespondence​(GeoSampleCorrespondence sampleCorrespondence)
        Parameters:
        sampleCorrespondence - The sampleCorrespondence to set.

      • getSubSeries

        public Collection<String> getSubSeries()
        Returns:
        the subSeries

      • getSummaries

        public String getSummaries()
        Returns:
        Returns the summaries.

      • setSummaries

        public void setSummaries​(String summary)

      • getSupplementaryFile

        public String getSupplementaryFile()
        Returns:
        String

      • setSupplementaryFile

        public void setSupplementaryFile​(String supplementaryFile)

      • setValues

        public void setValues​(GeoValues values)

      • getValues

        public GeoValues getValues​(Collection<GeoSample> s)
        Get a subset of the values. This is only used for 'splitting' a series.
        Parameters:
        s - Samples to include data from.
        Returns:
        geo values

      • getWebLinks

        public Collection<String> getWebLinks()
        Returns:
        Returns the webLinks.

      • setWebLinks

        public void setWebLinks​(Collection<String> webLinks)
        Parameters:
        webLinks - The webLinks to set.

      • isSubSeries

        public boolean isSubSeries()
        Returns:
        the isSubSeries

      • isSuperSeries

        public boolean isSuperSeries()
        Returns:
        the isSuperSeries

      • removeSamples

        public void removeSamples​(Collection<GeoSample> samplesToSkip)
        Clean up samples we have decided are ineligible (i.e., non transcriptomic)
        Parameters:
        samplesToSkip - the samples to remove

      • setContact

        public void setContact​(GeoContact contact)
        Parameters:
        contact - The contact to set.

      • setIsSubSeries

        public void setIsSubSeries​(boolean isSubSeries)
        Parameters:
        isSubSeries - the isSubSeries to set

      • setIsSuperSeries

        public void setIsSuperSeries​(boolean isSuperSeries)
        Parameters:
        isSuperSeries - the isSuperSeries to set